Good seating arrangement is good there now. LIRR is the only commuter railroad I know (besides SEPTA) to have 3+2 arrangement, especially compared to Europe where nothing is 3+2 on commuter railroads.
"Additionally, less seating and more standing room would increase capacity on any given train and reduce overcrowding."
If you're travelling a short distance, alright. But let's say you get in in Ronkonkoma in rush hour and you need to go to Penn. Rnkkm is crowded in rush hour and with less seats, you may not find a seat. So that means you would be standing the whole time. I bet you can't barely walk when you exit at Penn.
And that is only 1 branch, but there are several other crowded ones where you would have the same problem.